Hands-on summer school: Automated cloning, literature scraping, and research data management

From July 6th to 8th, 12 motivated participants from master students to staff scientists, came together in Ghent for the deCYPher hands-on summer school ‘Fundamentals in Integrating Synthetic Biology, Data, and AI,’ with participants joining from the University of Glasgow, KU Leuven, University of Primorska, UGent, and Isobionics.

Over three intensive days, the program wove together lab work, computational tools, and reflective discussion to introduce participants to the topics at the intersection of synthetic biology, data science, and artificial intelligence. Our partners VIB, UGent, and the Barcelona Supercomputing Center were closely involved in the teaching, bringing their expertise to the program.

Day one focused on building a solid foundation in synthetic biology, data, and AI. Participants got hands-on in the lab, running a molecular cloning session that introduced MEMOSA, a molecular cloning technique developed by the lab of Marjan De Mey. They then got their first look at a literature-scraping pipeline with Miguel Romero Durana from the Barcelona Supercomputing Center.

Day two dove even deeper into literature scraping. Participants explored how NLI embeddings and semantic models can be used to mine scientific literature for insights, with a particular focus on two complementary approaches: NLI and semantic models. NLI models assess whether one statement supports, contradicts, or is neutral toward another, making them well-suited to verifying specific claims. Semantic models capture meaning, allowing related concepts to be grouped even when the wording differs.

The final day centered on data management and FAIR principles, looking at how research data is managed and shared. Niels Geudens and Flora D’Anna from VIB led the workshop, which included a hands-on Lego exercise highlighting the importance of good research data documentation.

The final session was a World Café format focused on reflection and synthesis of the newly learned and giving participants space to discuss what an open science starter kit for synthetic biology might look like in practice.

Thank you to everyone who made this summer school such a success, the participants for their curiosity and engagement, and our partners VIB, UGent, and the Barcelona Supercomputing Center for leading the teaching throughout the program.

Molecular cloning taking over by a cloning robot

One of the clear highlights of the day was watching the automated cloning machine in action in Marjan De Mey’s lab, demonstrating how lab automation can look like.